Lab5 - CSci 3003: Introduction to Computing in Biology Lab...

Info iconThis preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
CSci 3003: Introduction to Computing in Biology Lab Assignment #5 20 points Assigned: 3/3/10 Due: 3/19/10 (before midnight) Goals of this lab: Practice writing programs to accomplish complex tasks. Practice regular expressions. Learn about gene expression regulation. Part I: Practice with regular expressions Write regular expressions for each of the following cases. Assume that the regular expression would be used in the following context, where we’d like to check if a string has a particular pattern, and if so, execute a set of statements: if($string =~ /pattern/) { <do something here> } a. Check to see if a string contains a valid yeast gene name, e.g. YJL045W, YKR034W, YLL023C (hint: a yeast ORF name consists of a Y, a letter between A and P, an R or L for right or left, 3 numbers, and then a W or C) b. Check to see if a yeast gene is encoded on the Crick strand (Remember, YHR143W-C is not encoded on the Crick strand!) c. Check a sequence string for Mot3’s (a yeast transcription factor) binding site motif: AAGG(G or T)T d. Check a sequence string for Hap1’s (a yeast transcription factor) binding site motif. ? implies that there is a single arbitrary nucleotide. GG???TA?CGG You can either write your answers in a script, or simply send them to us as text.
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Part II: Analyzing regulatory mechanisms behind cellular stress response For this problem, you will analyze the gene expression regulatory mechanisms behind the eukaryotic cellular response to stress. To do this, we will use data resulting from a genome- wide expression study in yeast, which was generated using a technology called microarrays. Briefly, microarrays enable scientists to simultaneously and quantitatively measure the
Background image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

Page1 / 4

Lab5 - CSci 3003: Introduction to Computing in Biology Lab...

This preview shows document pages 1 - 3. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online